Unit 5 Reflection

In this unit, "Walking the Dogma", we went more in depth about the structure of DNA and some of its jobs in copying itself as well as providing information for organism. We focused on how the nucleotides that make up DNA such as adenine, thymine, guanine, and cytosine are incorporated in the processes of DNA replication, protein synthesis, and gene regulation. Since I am a visual learner I was successful in grasping the concepts of DNA replication, protein synthesis, and gene regulation through diagrams and videos of these processes occurring.

<http://philschatz.com/anatomy-book/contents/m46073.html>

I am weaker in the RNA processing of eukaryotic gene regulation. I'm still not confident in the ideas of exons and introns and why its essential that introns are cut out of the sequence before it is read by the mRNA. Another idea that was difficult to wrap my head around was the idea of histons coiling around DNA and forming chromosomes. I became more confident with this concept, however, after watching a video of this happening. During this unit, I tried using my visual learning style to my advantage when we made a model of DNA and watched videos of the central dogma of biology. I realized that I really do remember information better when I use visual aids while I am first learning it. We learned about mutations occasionally occurring in protein synthesis, however, I still wonder why more mistakes are not made in this process. There are so many places for mistakes during transcription, the RNA traveling to the cytoplasm for translation, during translation, and the folding and producing of amino acids to make proteins. It is amazing to me that organisms preform with so few mistakes while doing such complex, multi-step processes.

<https://en.wikipedia.org/wiki/Point_mutation>

Protein Synthesis Lab

1) Proteins Synthesis is the process used to create proteins that involves DNA, RNA, and ribosomes. This process begins with transcription, in the nucleus, during which the DNA unzips, allowing the RNA polymerase to read and copy the DNA code for a mRNA. The mRNA then travels to the cytoplasm where translation occurs. Ribosomes read the mRNA 3 bases at a time in sequences known as codons. They then translate the codons into amino acids, eventually forming long chains of amino acids. These chains fold up and integrate with other amino acid chains until a protein is created.

<http://biologyteksbylauryncarter.weebly.com/protein-synthesis.html>

2) Generally, the mutation of substitution makes little to no change in the amino acid sequence. Frameshift mutation, however, seemed to have the greatest effect to the proteins. This type of mutation includes insertion and deletion, when a nucleotide is added or taken away. Where in the mRNA sequence the mutation occurs also has a great effect to the protein. The closer to the beginning of the sequence the mutation occurs, the more effect it will have on the protein. If the mutation occurs near the end, then only the final few amino acids will be affected, however, if the mutation occurs near the beginning, then the majority, if not all, of the amino acid sequence will be affected.

<https://en.wikipedia.org/wiki/Point_mutation>

3) I chose the mutation of deletion, in which I got rid of the very first nucleotide. This mutation was similar to a deletion mutation in step 4, in which I deleted a "T" near the begining of the sequence. I chose this mutation to prove my prediction correct that the closer to the beginning of the sequence the mutation occurs, the more the protein will be affected. This is because the earlier there is a mutation, the earlier the rest of the sequence will be out of order. A protein was never formed as a result of my mutation because there was no start codon.

4) Believe it or not, one common mutation in humans is blue eyes. Originally, all humans had brown eyes, however, around 10,000,000 years ago, a mutation occurred that limited the amount of melanin that could be produced in the stroma of the iris, leaving the stroma blue. Mutations can affect your life because it can prevent your body from developing traits required to properly function. 

<http://www.iran-daily.com/News/128325.html>

Unit 4 Reflection

This unit was all about genetics and the inheritance patterns of genes. Some common themes were genotypes and how they affect phenotypes, and homozygous vs heterozygous alleles. I feel strong in the concepts of mitosis and meiosis and the difference between genes, traits, DNA, and chromosomes. Some of my weaknesses include completing dihybrid punnet squares and fully grasping genetic exceptions such as gene linkage, epistasis, and polygenics. This unit I learned about time management when i designed my infographic, I made sure I had enough time to finish it. I feel more confident about the concepts in this unit because of the infographic we made. I discovered that making my own graphics helped me remember and understand genetics because I am a visual learner. After taking the VARK test, I discovered that I am mostly a visual learner, then a kinesthetic learner, then a reading and writing learner, and finally, an aural learner. I have taken a test similar to this one before and got the same results. I am not surprised that I am a visual leaner because I can remember diagrams and pictures better than words. To prepare for the upcoming test, I am going to draw pictures to help me remember biological concepts as well as using body movements to memorize genetic processes.

Coin Sex Lab Conclusion

In this lab, we used coins to simulate the randomness of chromosomes that go into sex. In meiosis, the chromosomes are split twice and make four new haploid cells. Each new haploid cell carries two alleles for each trait and one of these haploid cells actually participates in recombination. When we flipped the coins, we were simulating one of the four haploid cells, produced by meiosis, being chosen to have sex. The haploid cell that goes into sex gives those genes their offspring. To hypothesize about our results in this lab, we used probability to determine how likely different results were. Our expected results were exactly the same as our actual results for our dihybrid cross simulation. From this data I can conclude that alleles do indeed segregate independently, however some alleles tend to be inherited together, shown by the brown hair and brown eyes traits that were inherited together 9 out of 16 times. During our monohybrid simulation, we tested homozygous and heterozygous alleles having sex. Our results were very similar to our predictions. The limit of using probability is that one can only determine the probability of something happening and can never know for sure. For example if there is a 25% chance that your child will have a disorder, its a low probability, however, it is still entirely possible. Inheritance can also occur in two ways. Autosomal inheritance is when traits are inherited from one of the 44 non-sex chromosomes, such as the genes for bipolar disorder. X-linked inheritance is when traits are inherited from one of the 2 sex chromosomes, such as the genes for colorblindness. This can related to my life because I live among color blind people, and people with other disorders. This information can shift my world view on people because sex leaves you stuck and its not people's fault that they are disabled, they are the way they are simply because of sex and probability.

Genetics Infographic

Can be viewed larger at this link:

https://magic.piktochart.com/output/9065587-genetics

Unit 3 Reflection

Unit 3 was about cells. We focused on how cell's function, what they look like, and how they get their energy. It was easy for me to remember the parts of a cell required in making a protein and where they are located because of the analogy of each organelle being a part of a factory. It was more difficult to fully grasp and understand the processes involved for a cell to obtain energy. Cellular respiration is a process present in both plants and animals used to take food and turn it into energy, while photosynthesis is a process only in plants during which food is made from energy. Cellular respiration and photosynthesis are inverted. In this unit one of the in class activities was to draw and label the process of photosynthesis. This exercise made me realize what a high level of detail biology contains and the level of depth you can go into when studying the material. This made me a better student today than I was yesterday because I have learned that details are a crucial part but looking at the big picture is most important in understanding biology concepts. I am still left to wonder, however, what the proteins that cells make do in the body or plant. What role do they play that is so big that all the cells in the whole body have to help make them?

Egg Diffusion Lab Analysis

In this lab we answered the question: How and why does a cell's internal environment change, as it's external environment changes? We did this by placing one egg in a cup of sugar water and one egg in a cup of deionized water to see how these conditions would affect the egg. We measured the before and after circumference and mass of the eggs to find that the egg in sugar water shrunk and the egg in water grew.

1) As the sugar concentration increased the mass of the egg decreased by an average of 47.25% and the circumference decreased by an average of 22.94%. This change occurred because the sugar water solution was hypertonic to the egg, causing the egg to loose water and therefore shrink. The solvent of water diffuses from a lower concentration to a higher concentration to try to balance the amount of solvent and solute. However, the solute of sugar water couldn't move across the membrane into the egg because it's too large, causing the egg to only loose water and not gain sugar water.

2) The cell's internal environment changes as the external environment changes because cells naturally diffuse molecules in and out of its membrane through passive diffusion. Therefore, whatever molecules are outside the cell, this will affect what the concentration inside of the cell. When we put the egg in vinegar, it grew because vinegar is a solvent that diffused into the membrane. The external environment of the cell was the vinegar which affected the internal environment when the vinegar entered the cell, causing it to expand. However, when the egg was placed in sugar water, which is a solute, the egg shrunk because the solvent diffused out of the membrane to the external high concentration of solute outside the cell.

3) This lab demonstrates the biological principle of passive diffusion. During passive diffusion, transport proteins act as pores that allow molecules to slide through like a straw. This diffusion also acts as a filter because molecules that are too large cannot diffuse through the transport proteins. The solute of sugar water cannot passively diffuse through the cell membrane because its molecules are too large.

4) Fresh vegetables are sprinkled with water at markets to maintain turgor pressure. The vegetables look more appealing to customers when they are not shriveled up and water diffuses into the vegetables, causing them to expand. As humans, we shouldn't drink too much salt water because it causes our cells to loose water. The water in our cells diffuses to the high concentration of salt outside the cell, causing our cells to shrink and eventually die. Similarly, the plants along the side of the road shrivel up when salted because the water inside the plant cells diffuses out.

5) I would create an experiment testing whether plant and animal cells react the same when placed in sugar water. Would they both loose the same amount of water? Would they loose water at the same rate? I would test for the difference of diffusion in plant and animal cells.

Egg Cell Macromolecules Lab Conclusion

In this lab we asked the question: Can macromolecules be identified in an egg cell? We found that there are proteins in the egg membrane, polysaccharides in the egg white, and lipids in the egg yolk. Proteins had a 4 out of 10 color change in the egg membrane. The membrane turned the color purple when sodium hydroxide and copper sulfate were added to it because of the presence of proteins. This is because of transport proteins are present in the membrane to that let things in and out of the cell. This data supports our claim that proteins are in the membrane because they serve as "gateways" to diffuse molecules into the cell. Polysaccharides had a 5 out of 10 color change in the egg white. The egg white turned black when iodine was added because of the polysaccharides. They tested positive in the egg white because polysaccharides store energy and serve as food that surrounds the chick in the egg yolk. The data supports our claim that polysaccharides are present in the egg white because polysaccharides have a useful function in the egg white as energy. Lipids had a 5 out of 10 color change in the egg yolk. The yolk turned orange when Sudan 3 and water were added because of the presence of lipids. Lipids were found in the yolk because the membrane surrounding the yolk is made up of phospholipids. This data supports our claim because lipids are essential in the yolk to keep it enclosed and separate from the egg white.

Our data was not as accurate as it could have been because of a few possible errors. One possible error is the amount of membrane each tester ripped off to test. The procedures of the experiment gave a milliliter amount of membrane to test which left students guessing how much membrane to use because the membrane is not liquid and can not be measured in milliliters. Most testers ended up guessing how much to use by ripping a small piece off. This affected our results because if the tester didn't use a large enough sample of the egg membrane, some of the macromolecules could have not tested positive because there were not enough of that molecule on the small sample used. In future experiments I would recommend editing the procedures to give a weight measurement for students to weigh the sample of membrane to make sure a large enough sample is used. Another possible error is that there was no timing instructed for how long to wait for each part of the egg to change color. Some tester may have been in more of a rush and didn't give their samples a long enough time to test color. This affected the experiment because some of the macromolecules that were present didn't test positive because not enough time was given for them to change color. For future experiments I would recommend adding a time in the procedures to clarify how long to wait for color change.

The purpose of this lab was to demonstrate the presence of macromolecules in different parts of the cell by testing an egg. From this lab I learned about the connection between the function and location of the four macromolecules which helps me understand how the macromolecules help cells function. Based on my experience with this lab I now am aware that eggs are incredible healthy because they contain all four macromolecules that are all crucial to the nutrition of our bodies.

The 20 Big Questions in Science

A big question of science I am interested in is are we alone in the universe? This questions interests me because everyone on the Earth goes about their lives thinking that the Earth is all we have and there is no other option or other way of living. If there are other planets that sustain life out in the universe that leaves me to wonder about the technological advancement of the planet and what ideas and concepts they hold that we have yet to discover. I wonder what the life there looks like, would there be humans ? A current hypothesis for this question could be: If scientists don't know what exists in the majority of the universe, then there is a possibility that life on earth is not the only life in the universe.

My 20 Big Questions:

1) What is the purpose of life?
2) Could a computer have a mind?
3) What happens after death?
4) What is reality?
5) Do we have free will?
6) Will we ever have a theory of everything?
7) What comes after homosapiens?
8) Who am I?
9) What is time?
10) Is there such a thing as fate/destiny?
11)Why do we suffer?
12) Is there a God?
13) Will the world end?
14) Where do germs come from?
15) Is aging inevitable?
16) How are bodies able to repair themselves?
17) Why have humans evolved music?
18) How are there so many types of materials?
19) How did life come about?
20) Are there other universes?

Identifying Questions and Hypotheses

I found an experiment about how the brain encodes time and place. This experiment, done at the Massachusetts Institute of Technology identified the "where" and "when" components of memory. <www.sciencedaily.com/releases/2015/09/150923134112.htm>. The question of the study was what brain circuit processes the "when" and "where components of memory? They reached the hypothesis that if the entorhinal cortex seperates location and time, then the "when" and "where" information of memory is split even before it reaches the hippocampus. Prior to this experiment, it was believed that the memory storage part of the brain, the hippocampus, separated the timing and context information. However, this hypothesis was based on the idea that the circuit, which connects the hippocampus and a region of the cortex known as entorhinal cortex, separates location and timing into two streams of information before it reaches the hippocampus. 

Unit 2 Reflection

Unit two was all about chemistry and understanding concepts about everything from parts of an atom to enzymes and how they create chemical reactions. The chemistry we learned about all relates directly to biology and will help us better understand life. One main topic covered in two different vodcasts were the four macro molecules. This included carbohydrates, Lipids, Proteins, and Nucleic acids. An essential concept that I had success remembering was the structure and function of each macro molecule. We also covered material about basic chemistry such as different types of bonds and acids and bases in the first vodcast. These concepts are harder for me to remember and are one of my weaknesses in this unit. Finally we went in depth about enzymes and how they speed up chemical reaction using activation energy. We completed a lab during which we made cheese from milk and rennin while testing many different pH and temperature variables. During this lab I learned that enzymes get activation energy from warm and highly acidic environments. This relates to real life examples of cheese companies and laundry solution companies who use enzymes on a daily basis to make their product. This unit made me a better student today because I feel that the HOT questions and relate & reviews made me think about the concepts more in depth and I now remember the material better. I also learned about being aware of possible error in an experiment while I am doing the experiment. During the cheese lab Mr. Orre reminded us to be thinking about what errors could be happening and I wrote them down, making it easier for me while I was completing my conclusion because I already had my errors thought of. This unit leaves me thinking about how many aspects of life the four macro molecules are found in. They are the four big groups of molecules and so I am left to wonder if they are literally in every organic material or just in a few. I also wonder how these macro molecules were discovered and who analyzed them to figure out there were four types. This unit taught me lab skills as well as crucial chemistry concepts.

Cheese Lab Conclusion

In this lab we asked the question what are the optimal conditions and curdling agents for making cheese. We found that chymosin is the best agent and is optimal in a hot and acidic environment. Chymosin curdled 5 minutes faster than rennin in a pH controlled environment and curdled in 20 minutes in a base environment while rennin didn’t curdle at all. Chymosin makes products very quickly, making it the most efficient curdling agent for making cheese. Chymosin is made from rennin and rennin is extracted from calf stomachs where conditions are very hot and highly acidic. This is why chymosin is optimal in warm acidic conditions and supports our claim that chymosin is the best agent in a hot and acidic environment.

Our data contradicts the expected results because of the uneven timing of heating and checking our test tubes. A possible error was when we took the test tubes out of our armpits to check for curdling every 5 minutes. The curdling may have occurred in 3 minutes but we didn’t know because we only checked after 5 minutes of being in our armpits. This affected our results and made them inaccurate because our data states that chymosin, rennin, and buttermilk all took 5 minutes to curdle in an acidic environment, however, chymosin might have curdled faster than rennin and buttermilk but we don’t know for sure because we only checked 5 minutes into the curdling process. To improve this lab you could check the test tube every minute instead of every 5 minutes to find more accurate results about the exact time the curdling occurred. Another possible error is that people have varying body temperatures and when putting the test tube in your armpit, everyone is putting their test tubes in different temperatures. Not only are body temperatures of everyone different, but depending on how many layers of clothing everyone had one, the temperatures varied. This affected the results because one of the constants of the experiment was the temperature the test tubes were in and with that constant becoming a variable, the results become inaccurate. In the future of this experiment the biologists should immerge all the test tubes in a pot of hot water or a different heating source where they all the test tubes are heated at the same temperature.

This lab was done to demonstrate what the optimal conditions and curdling are for making cheese. From this lab I learned that curdling occurs in very warm and acidic environments which helps me understand the concept of activation energy and finding the right conditions for activation energy to cause enzymes to begin making products. Based on my experience with this lab if I am ever baking and the recipe calls for buttermilk I can just add lemon juice to regular milk and I will have buttermilk. The acidic lemon juice makes bacteria appear and enzymes form and begin to make chemical reactions, giving it a sour taste.

Time in minutes
Curdling Agent:	chymosin	rennin	buttermilk	mik (control)
Acid	5	5	5
Base	20
pH control	15	10
Cold
Hot	5	5
Average	10	10

Sweetness Lab Analysis

1. The structure of a carbohydrate affects its taste because the more rings on a carbohydrate, the less sweet is will be. Monosaccharides are the sweetest of the carbohydrates with degrees of sweetness ranging from 60 out of 200 to 200 out of 200. Disaccharides are semi-sweet carbohydrates with degrees of sweetness ranging from 10 out of 200 to 100 out of 200. Polysacchrides are carbohydrates that are not sweet and all have a deggree of sweetness of 0 out of 200. For example, fructose is a monosaccharide that has a sweetness of 200 out of 200 while starch is a polysaccharide that has a sweetness of 0 out of 200. This data support the fact that monosaccharides are the sweetest carbohydrate, disaccharides are semi-sweet carbohydrates, and polysaccharides are carbohydrates with no sweetness. My hypothesis was supported that if sucrose is naturally found in fruits and vegetables, it will be sweet. Sucrose is a disaccharide that has a sweetness of 100 out of 200. This hypothesis also supports my reasoning that disaccharides are semi-sweet carbohydrates.

2. The structure of carbohydrates are rings of hydrogen, carbon, and oxygen. Different types of carbohydrates have different numbers of rings for different purposes. For example, cellulose, a polysaccharide, has multiple rings which it uses to make cell walls. Since there are many rings, there are enough to build an entire wall around the cell. Monosaccharides, however have more simple uses because they only have one ring. Glucose, a monosaccharide is used by cells as a primary source of energy. The structure of carbohydrates suggest whether they are used for simple or more complex tasks.

3. No, all of the testers gave each sample a different rating. One reason this occurred is because each person has unique senses and everyone tastes slightly different. What is sweet for one person may not be sweet at all for another person. Another reason is because there was no given scale to inform everyone what a 200 sweetness tasted like and what a 100 sweetness tasted like. Therefore, everyone's analytical thinking to determine what measurement of sweetness each carbohydrate was different. A third reason that everyone gave the samples a different rating is because we did not cleanse our palette between tastings. Depending on the order in which each person tasted the sugars, the carbohydrates' sweetness was based on what carbohydrate they tasted before.

4. "Savory dishes that taste of broth evoke pleasant emotions in most people. They are a signal that the food is rich in protein...flavors that are appetizing increase the production of saliva and gastric juices, making them truly mouthwatering...The chemical substance responsible for the taste is freed in the mouth and comes into contact with a nerve cell. It activates the cell by changing specific proteins in the wall of the sensory cell. This change causes the sensory cell to transmit messenger substances, which in turn activate further nerve cells. These nerve cells then pass information for a particular perception of flavor on to the brain." Humans taste sweetness because of taste buds on the tongue that send sensory information to the brain. Tasters rank sweetness differently because everyone's cells transmit information differently and at different speeds, causing information people think to vary.


"How Does Our Sense of Tast Work?" How Does Our Sense of Taste Work? U.S. National Library of Medicine, 28 Oct. 2009. Web. 15 Sept. 2015. <http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0072592/>.

 

Biology Collage

Jean Lab Conclusion

    Jean Lab Conclusion

Ella Foster

In this lab we asked the question “What concentration of bleach is best to fade the color out of new denim material in 10 minutes without visible damage to the fabric?” We found that a combination of 50% bleach and 50% water faded the color out of the denim without damaging it. The 50% bleached denim showed a significant color fade with an overall average of 5.3 out of 10. The 50% also had good quality and didn’t show any visible damage with an average of 3.3 out of 10. Bleach changes the integrity of fabrics and is commonly used to remove stains from white clothing. Bleach is also a cleaning agent used to clean mold off of pavement, patios, and other surfaces. This data supports our claim because since bleach is such a strong substance, bleaching jeans with 100% bleach damages them. Therefore, a 50% concentration of bleach is the perfect amount of bleach to fade denim without damage.

    Our data contradicts the expected results because of the way we layered the denim while submerging them in bleach, didn’t accurately measure the graduated cylinders, and didn’t completely rinse the denim to stop the bleaching process. The petri dishes were not tall enough to completely submerge all three 5x5 pieces of denim and therefore the denim on the top of the pile of denim squares weren’t soaked in as much bleach as the other two. The effect of this was that when we averaged the three pieces of denim for quantitative data, one denim piece pulled down our average because it didn’t fade and damage as much as a result of it lying on top of the pile in the petri dish. The error of measuring the graduated cylinders was caused because we only had about an hour to do the experiment and we weren’t as careful as we could have been about measuring the bleach and water in the graduated cylinder accurately. This effected our experiment because it may have lowered or highered the amount of water and/or bleach in each petri dish, changing the results we received. Finally, we did not rinse the pieces of denim three times in water to completely stop the bleaching process as directed in the procedures because we ran out of time. Failing to fully rinse the pieces of denim altered the results of the experiment because our denim was exposed to the bleach longer than it should have been, making the jean material more damaged and color faded. Due to these errors, in future experiments I would recommend giving yourself more than an hour to correctly measure the liquids and fully rinse the jeans. I would also suggest to use three petri dishes per concentration of bleach to give each piece of denim its own dish.

    This lab was done to demonstrate the correct method to fade denim at home using bleach. From this lab I learned the intense staining power that the chemical substance of bleach has which helps me understand the dangers of overusing it on clothing and other surfaces prone to stain. Based on my experience from this lab I will always be cautious around bleach and if I ever wish to fade or clean my clothing I will take precautionary steps to not damage the material.

Concentration (% Bleach)	Average Color Removal (Scale 1-10)	Average Fabric Damage (Scale 1-10)
100	8.6	5
50	5.3	3.3
25	2.3	1.3
12.5	1.6	1
0	0	0

 Link To Acess from Google docs:


https://docs.google.com/document/d/1Mr2Kbh2RY5EUV-LrRXFQ7Bxtz0NmuJpOXXcpAH16aPw/edit